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    On 31/01/2012 2:59 PM, Li SUN wrote:
    <blockquote
cite="mid:CAOmm63LWkomnV0rOTdvQM_m0GYEBKv1Kh1h=4+aGd1N3RK4=ng@mail.gmail.com"
      type="cite">So please look at the attached figure which is exactly
      the leftmost subfigure of Figure 4.8 from manual. Given one plane
      defined by (j,k,l), the cases where &lt;case1&gt; i is above the
      plane and &lt;case2&gt; below the plane can give the same dihedral
      angles.</blockquote>
    <br>
    Only if they are measured in a unsigned fashion.<br>
    <br>
    <blockquote
cite="mid:CAOmm63LWkomnV0rOTdvQM_m0GYEBKv1Kh1h=4+aGd1N3RK4=ng@mail.gmail.com"
      type="cite"> But chirality can distinguish the two cases: define
      chirality = ( (lk) x (kj) ) . (ji), then chirality is positive for
      &lt;case1&gt; and negative for &lt;case2&gt;. Am I right?<br>
    </blockquote>
    <br>
    During the flipping process, the energy/force from the dihedral
    restraint potential will increase because the angle deviates from
    the programmed one. This will act to prevent flipping occurring
    without needing to trouble with computing a signed dihedral angle.
    If you pull too hard, then the restraint has insufficient effect.
    Choose wisely.<br>
    <br>
    Mark<br>
    <br>
    <blockquote
cite="mid:CAOmm63LWkomnV0rOTdvQM_m0GYEBKv1Kh1h=4+aGd1N3RK4=ng@mail.gmail.com"
      type="cite">
      <br>
      <br>
      <br>
      <br>
      <div class="gmail_quote">On Mon, Jan 30, 2012 at 6:01 PM, Mark
        Abraham <span dir="ltr">&lt;<a moz-do-not-send="true"
            href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>&gt;</span>
        wrote:<br>
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          0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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            <div class="im"> On 31/01/2012 11:53 AM, Li SUN wrote:
              <blockquote type="cite">Hello,<br>
                <br>
                I am doing pulling simulations with GROMACS and would
                like to keep the chirality of the protein along the
                trajectory otherwise the protein will take the wrong
                chirality especially at long extensions. I have checked
                that using the improper dihedral or dihedral restraint
                can restrain the dihedral, but dihedral restraint is not
                equivalent to chirality restraint.</blockquote>
              <br>
            </div>
            Why not? See 4.2.11 of manual and figure 4.8.<span
              class="HOEnZb"><font color="#888888"><br>
                <br>
                Mark</font></span>
            <div class="im"><br>
              <br>
              <blockquote type="cite"> So I am wondering if there is a
                "chirality restraint" somewhere in GROMACS. Otherwise I
                might have to modify the code...<br>
                <br>
                Thanks in advance!<br>
                <br clear="all">
                <br>
                -- <br>
                Li Sun<br>
                Department of Physics<br>
                University of California, San Diego<br>
                <br>
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                <br>
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          <br>
          --<br>
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        </blockquote>
      </div>
      <br>
      <br clear="all">
      <br>
      -- <br>
      Li Sun<br>
      Department of Physics<br>
      University of California, San Diego<br>
      <br>
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